Physical Sciences and Mathematics Commons^™

Three X-Ray Transients In M31 Oberserved With Swift, R. Voss, W. Pietsch, F. Haberl, H. Stiele, J. Greiner, G. Sala, Dieter H. Hartmann, D. Hatzidimitriou

Publications

Aims.The purpose of this study is to find transient X-ray sources in M 31, and to investigate and classify their nature.Methods.Three X-ray transients were observed with Swift. For each of the three X-ray transients we use the Swift X-ray and opticaldata together with observations from XMM-Newton and Chandra to investigate the lightcurves and the spectra of the outburst, andthereby to identify the source types. Results.The outburst of XMMU J004215.8+ 411924 lasted for about one month. The source had a hard power-law spectrum with aphoton index of 1.6. It was previously identified as a Be/X-ray binary based on the optical identification …

Supernova Neutrino Nucleosynthesis Of Light Elements With Neutrino Oscillations, Takashi Yoshida, Toshitaka Kajino, Hidekazu Yokomakura, Keiichi Kimura, Akira Takamura, Dieter H. Hartmann

Publications

Light element synthesis in supernovae through neutrino-nucleus interactions, i.e., the ν-process, is affected by neutrino oscillations in the supernova environment. There is a resonance of 13-mixing in the O/C layer, which increases the rates of charged-current ν-process reactions in the outer He-rich layer. The yields of 7Li and 11B increase by about a factor of 1.9 and 1.3, respectively, for a normal mass hierarchy and an adiabatic 13-mixing resonance, compared to those without neutrino oscillations. In the case of an inverted mass hierarchy and a non-adiabatic 13-mixing resonance, the increase in the 7Li and 11B yields is much smaller. Observations …

Towards A System For Controlling Client-Server Traffic In Virtual Worlds Using Sdn, Jason Anderson, Jim Martin

Publications

Scaling virtual worlds in the age of cloud computing is complicated by the problem of efficiently directing client-server traffic in the face of agile and dynamic compute resources. In this proposed model, Software Defined Networking and compact encoding of avatar data in packet headers are combined to make a fast, scalable, high capacity proxy server that can hide the server infrastructure while fitting well with the IaaS paradigm of modern cloud providers.

Grb 091024a And The Nature Of Ultra-Long Gamma-Ray Bursts, F. J. Virgili, C. G. Mundell, V. Pal'shin, C. Guidorzi, R. Margutti, A. Melandri, R. Harrison, S. Kobayashi, R. Chornock, A Henden, A C. Updike, S B. Cenko, N R. Tanvir, I A. Steele, A Cucchiara, A Gomboc, A Levan, Z Cano, C J. Mottram, N R. Clay, D Bersier, D Kopac, J Japelj, A V. Filippenko, W Li, D Svinkin, S Golenetskii, Dieter H. Hartmann, P A. Milne, G Williams, P T. O'Brien, D B. Fox, E Berger

Publications

We present a broadband study of gamma-ray burst (GRB) 091024A within the context of other ultra-long-duration GRBs. An unusually long burst detected by Konus–Wind (KW), Swift, and Fermi, GRB 091024A has prompt emission episodes covering ∼1300 s, accompanied by bright and highly structured optical emission captured by various rapid-response facilities, including the 2 m autonomous robotic Faulkes North and Liverpool Telescopes, KAIT, S-LOTIS, and the Sonoita Research Observatory. We also observed the burst with 8 and 10 m class telescopes and determine the redshift to be z = 1.0924 ± 0.0004. We find no correlation between the optical and γ-ray …

High-Resolution Near-Infrared Spectroscopy Of Hd 100546. I. Analysis Of Asymmetric Ro-Vibrational Oh Emission Lines, Joseph Liskowsky, Sean D. Brittain, Joan R. Najita, John S. Carr, Greg W. Doppman, Matthew R. Troutman

Publications

We present observations of ro-vibrational OH and CO emission from the Herbig Be star HD 100546. The emission from both molecules arises from the inner region of the disk extending from approximately 13 AU from the central star. The velocity profiles of the OH lines are narrower than the velocity profile of the [O i] λ6300 line, indicating that the OH in the disk is not cospatial with the Oi. This suggests that the inner optically thin region of the disk is largely devoid of molecular gas. Unlike the ro-vibrational CO emission lines, the OH lines are highly asymmetric. We …

High-Resolution Near-Infrared Spectroscopy Of Hd 100546. Ii. Analysis Of Variable Rovibrational Co Emission Lines, Sean D. Brittain, Joan Najita, John S. Carr, Joseph Liskowsky, Matthew R. Troutman, Greg W. Doppmann

Publications

We present observations of rovibrational CO in HD 100546 from four epochs spanning 2003 January through 2010 December. We show that the equivalent widths of the CO lines vary during this time period with the v = 1–0 CO lines brightening more than the UV fluoresced lines from the higher vibrational states.While the spectroastrometric signal of the hot band lines remains constant during this period, the spectroastrometric signal of the v = 1–0 lines varies substantially. At all epochs, the spectroastrometric signals of the UV fluoresced lines are consistent with the signal one would expect from gas in an axisymmetric …

Preferential Scattering By Interfacial Charged Defects For Enhanced Thermoelectric Performance In Few-Layered N-Type Bi2te3, Pooja Puneet, Ramakrishna Podila, Mehmet Karakaya, Song Zhu, Jian He, Terry M. Tritt, Mildred S. Dresselhaus, Apparao Rao

Publications

Over the past two decades several nano-structuring methods have helped improve the figure of merit (ZT) in the state-of-the art bulk thermoelectric materials. While these methods could enhance the thermoelectric performance of p-type Bi₂Te₃, it was frustrating to researchers that they proved ineffective for n-type Bi₂Te₃ due to the inevitable deterioration of its thermoelectric properties in the basal plane. Here, we describe a novel chemical-exfoliation spark-plasma-sintering (CE-SPS) nano-structuring process, which transforms the microstructure of n-type Bi₂Te₃ in an extraordinary manner without compromising its basal plane …

Molecular Mechanisms Of Disease-Causing Missense Mutations, Shannon Stefl, Hafumi Nishi, Marharyta Petukh, Anna R. Panchenko, Emil Alexov

Publications

Genetic variations resulting in a change of amino acid sequence can have a dramatic effect on stability, hydrogen bond network, conformational dynamics, activity and many other physiologically important properties of proteins. The substitutions of only one residue in a protein sequence, so-called missense mutations, can be related to many pathological conditions, and may influence susceptibility to disease and drug treatment. The plausible effects of missense mutations range from affecting the macromolecular stability to perturbing macromolecular interactions and cellular localization. Here we review the individual cases and genome-wide studies which illustrate the association between missense mutations and diseases. In addition we …

Broadband Monitoring Tracing The Evolution Of The Jet And Disk In The Black Hole Candidate X-Ray Binary Maxi J1659-152, A. J. Horst, P. A. Curran, J. C. A. Miller-Jones, J. D. Linford, J. Gorosabel, D. M. Russell, A. De Ugarte Postigo, A. A. Lundgren, G. B. Taylor, D Maitra, S Guziy, T M. Belloni, C Kouveliotou, P G. Jonker, A Kamble, Z Paragi, J Homan, E Kuulkers, J Granot, D Altamirano, M M. Buxton, A Castro-Tirado, R P. Fender, M A. Garrett, N Gehrels, Dieter H. Hartmann, J A. Kennea, H A. Krimm, V Mangano, E Ramirez-Ruiz, P Romano, R.A.M.J. Wijers, R Wijnands, Y J. Yang

Publications

MAXI J1659−152 was discovered on 2010 September 25 as a new X-ray transient, initially identified as a gamma-ray burst, but was later shown to be a new X-ray binary with a blackhole as the most likely compact object. Dips in the X-ray light curves have revealed that MAXI J1659−152 is the shortest period black hole candidate identified to date. Here we present the results of a large observing campaign at radio, submillimetre, near-infrared (nIR), optical and ultraviolet (UV) wavelengths. We have combined this very rich data set with the available X-ray observations to compile a broad-band picture of the evolution …

Near-Infrared Spectroscopic Study Of V1647 Ori, Sean D. Brittain, T W. Rettig, Theodore Simon, Erika L. Gibb, Joseph Liskowsky

Publications

We present new high-resolution infrared echelle spectra of V1647 Ori, the young star that illuminates McNeil's nebula. From the start, V1647 Ori has been an enigmatic source that has defied classification, in some ways resembling eruptive stars of the FUor class and in other respects the EXor variables. V1647 Ori underwent an outburst in 2003 before fading back to its pre-outburst brightness in 2006. In 2008, it underwent a new outburst. In this paper we present high-resolution K-band and M-band spectra from the W. M. Keck Observatory that were acquired during the 2008 outburst. We compare the spectra to spectra …

Nitrogen Abundances And The Distance Moduli Of The Pleiades And Hyades, Blake Miller, Jeremy R. King, Yu Chen, Ann Merchant Boesgaard

Publications

Recent reanalyses of HIPPARCOS parallax data confirm a previously noted discrepancy with the Pleiades distance modulus estimated from main-sequence fitting in the color-magnitude diagram. One proposed explanation of this distance modulus discrepancy is a Pleiades He abundance that is significantly larger than the Hyades value. We suggest that, based on our theoretical and observational understanding of Galactic chemical evolution, nitrogen abundances may serve as a proxy for helium abundances of disk stars. Utilizing high-resolution near-UV Keck/HIRES spectroscopy, we determine N abundances in the Pleiades and Hyades dwarfs from NH features in the λ3330 region. While our Hyades N abundances show …

Gas Lines From The 5-Myr Old Optically Thin Disk Around Hd141569a, W F. Thi, C Pinte, E Pantin, J C. Augereau, G Meeus, F Menard, C Martin-Zaidi, P Woitke, P Riviere-Marichalar, I Kamp, A Carmona, G Sandell, C Eiroa, W Dent, B Montesinos, G Aresu, R Meijerink, M Spaans, G White, D Ardila, J Lebreton, I Mendigutia, Sean D. Brittain

Publications

At the distance of 99-116 pc, HD141569A is one of the nearest HerbigAe stars that is surrounded by a tenuous disk, probably in transition between a massive primordial disk and a debris disk. We observed the fine-structure lines of OI at 63 and 145 micron and the CII line at 157 micron with the PACS instrument onboard the Herschel Space Telescope as part of the open-time large programme GASPS. We complemented the atomic line observations with archival Spitzer spectroscopic and photometric continuum data, a ground-based VLT-VISIR image at 8.6 micron, and 12CO fundamental ro-vibrational and pure rotational J=3-2 observations. We …

Accretion Variability Of Herbig Ae/Be Stars Observed By X-Shooter Hd 31648 And Hd 163296, I Mendigutia, Sean D. Brittain, C Eiroa, G Meeus, B Montesinos, A Mora, J Muzerolle, R D. Oudmaijer, E Rigliaco

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This work presents X-Shooter/Very Large Telescope spectra of the prototypical, isolated Herbig Ae stars HD 31648 (MWC 480) and HD 163296 over five epochs separated by timescales ranging from days to months. Each spectrum spans over a wide wavelength range covering from 310 to 2475 nm. We have monitored the continuum excess in the Balmer region of the spectra and the luminosity of 12 ultraviolet, optical, and near-infrared spectral lines that are commonly used as accretion tracers for T Tauri stars. The observed strengths of the Balmer excesses have been reproduced from a magnetospheric accretion shock model, providing a mean …

Magnetic Field Generation In A Jet-Sheath Plasma Via The Kinetic Kelvin-Helmholtz Instability, K.-I. Nishikawa, P. Hardee, B. Zhang, I. Dutan, M. Medvedev, E. J. Choi, K. W. Min, J. Niemiec, Y. Mizuno, A Nordlund, J T. Frederiksen, H Sol, M Pohl, Dieter H. Hartmann

Publications

We have investigated the generation of magnetic fields associated with velocity shear between an unmagne-tized relativistic jet and an unmagnetized sheath plasma. We have examined the strong magnetic fields generated by ki-netic shear (Kelvin–Helmholtz) instabilities. Compared to the previous studies using counter-streaming performed by Alves et al. (2012), the structure of the kinetic Kelvin– Helmholtz instability (KKHI) of our jet-sheath configura-tion is slightly different, even for the global evolution of the strong transverse magnetic field. In our simulations the major components of growing modes are the electric field Ez, perpendicular to the flow boundary, and the magnetic field By, transverse …

A Spectroscopic Analysis Of The Eclipsing Short-Period Binary V505 Persei And The Origin Of The Lithium Dip, Patrick Baugh, Jeremy R. King, Constantine P. Deliyannis, Ann Merchant Boesgaard

Publications

As a test of rotationally-induced mixing causing the well-known Li dip in older mid-F dwarfs in the local Galactic disk, we utilize high-resolution and -S/N Keck/HIRES spectroscopy to measure the Li abundance in the components of the ∼1 Gyr, [Fe/H]= −0.15 eclipsing short-period binary V505 Per. We find A(Li) ∼ 2.7 ± 0.1 and 2.4 ± 0.2 in the Teff∼6500 and 6450K primary and sec-ondary components, respectively. Previous Teff determinations and uncertainties suggest that each component is located in the midst of the Li dip. If so, their A(Li) are ≥2–5 times larger than A(Li) detections and upper limits observed …

Continuous Development Of Schemes For Parallel Computing Of The Electrostatics In Biological Systems: Implementation In Delphi, Chuan Li, Marharyta Petukh, Lin Li, Emil Alexov

Publications

Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano-objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano-objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (J Comput Chem. 2012 Sep 15; 33(24):1960–6.) to include parallelization …

Cancer Missense Mutations Alter Binding Properties Of Proteins And Their Interaction Networks, Hafumi Nisha, Manoj Tyagi, Shaolei Teng, Benjamin A. Shoemaker, Kosuke Hashimoto, Emil Alexov, Stefan Wuchty, Anna R. Panchenko

Publications

Many studies have shown that missense mutations might play an important role in carcinogenesis. However, the extent to which cancer mutations might affect biomolecular interactions remains unclear. Here, we map glioblastoma missense mutations on the human protein interactome, model the structures of affected protein complexes and decipher the effect of mutations on protein-protein, protein-nucleic acid and protein-ion binding interfaces. Although some missense mutations over-stabilize protein complexes, we found that the overall effect of mutations is destabilizing, mostly affecting the electrostatic component of binding energy. We also showed that mutations on interfaces resulted in more drastic changes of amino acid physico-chemical …

The Role Of Protonation States In Ligand-Receptor Recognition And Binding, Marharyta Petukh, Shannon Stefl, Emil Alexov

Publications

In this review we discuss the role of protonation states in receptor-ligand interactions, providing experimental evidences and computational predictions that complex formation may involve titratable groups with unusual pKa’s and that protonation states frequently change from unbound to bound states. These protonation changes result in proton uptake/release, which in turn causes the pHdependence of the binding. Indeed, experimental data strongly suggest that almost any binding is pH-dependent and to be correctly modeled, the protonation states must be properly assigned prior to and after the binding. One may accurately predict the protonation states when provided with the structures of the unbound …

X-Ray Source Variability Study Of The M31 Central Field Using Chandra Hrc-1, F. Hofmann, W. Pietsch, M. Henze, F. Haberl, R. Sturm, M. Della Valle, Dieter H. Hartmann, D. Hatzidimitriou

Publications

Context. The central field of the Andromeda galaxy (M 31) has been monitored, using the Chandra HRC-I detector (about 0.1-10 keV energy range) from 2006 to 2012 with the main aim to detect X-rays from optical novae. We present a systematic analysis of all X-ray sources found in the 41 nova monitoring observations, along with 23 M 31 central field HRC-I observations available from the Chandra data archive starting in December 1999. Aims. Based on these observations, we studied the X-ray long-term variability of the source population and especially of X-ray binaries in M 31. Methods. We created a catalogue …

Nature Of The Gas And Dust Around 51 Oph, W F. Thi, F Menard, G Meeus, A Carmona, P Riviere-Marichalar, J C. Augereau, I Kamp, P Woitke, C Pinte, I Mendigutia, C Eiroa, B Montesinos, Sean D. Brittain, W Dent

Publications

Circumstellar disc evolution is paramount for the understanding of planet formation. The GASPS program aims at determining the circumstellar gas and solid mass around ~250 pre-main-sequence Herbig Ae and TTauri stars. We aim to understand the origin and nature of the circumstellar matter orbiting 51 Oph, a young (Myr) luminous B9.5 star. We obtained continuum and line observations with the PACS instrument on board the Herschel Space Observatory and continuum data at 1.2 mm with the IRAM 30m telescope. The SED and line fluxes were modelled using the physico-chemo radiative transfer code ProDiMo. We detected a strong emission by OI …

Nanobiotechnology Can Boost Crop Production And Quality: First Evidence From Increased Plant Biomass, Fruit Yield And Phytomedicine Content In Bitter Melon (Momordica Charantia), Chittaranjan Kole, Phullara Kole, K Manoj Randunu, Poonam Choudhary, Ramakrishna Podila, Pu Chen Ke, Apparao M. Rao, Richard K. Marcus

Publications

BACKGROUND:

Recent research on nanoparticles in a number of crops has evidenced for enhanced germination and seedling growth, physiological activities including photosynthetic activity and nitrogen metabolism, mRNA expression and protein level, and also positive changes in gene expression indicating their potential use in crop improvement. We used a medicinally rich vegetable crop, bitter melon, as a model to evaluate the effects of seed treatment with a carbon-based nanoparticle, fullerol [C60(OH)20], on yield of plant biomass and fruit characters, and phytomedicine contents in fruits.

RESULTS:

We confirmed the uptake, translocation and accumulation of fullerol through bright field imaging and Fourier transform …

Progress In Developing Poisson-Boltzmann Equation Solvers, Chuan Li, Marharyta Petukh, Emil Alexov

Publications

This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to …

A Rational Free Energy-Based Approach To Understanding And Targeting Disease-Causing Missense Mutations., Zhe Zhang, Shawn Witham, Marharita Petukh, Gautier Moroy, Maria Miteva, Yoshihiko Ikeguchi, Emil Alexov

Publications

BACKGROUND AND SIGNIFICANCE:

Intellectual disability is a condition characterized by significant limitations in cognitive abilities and social/behavioral adaptive skills and is an important reason for pediatric, neurologic, and genetic referrals. Approximately 10% of protein-encoding genes on the X chromosome are implicated in intellectual disability, and the corresponding intellectual disability is termed X-linked ID (XLID). Although few mutations and a small number of families have been identified and XLID is rare, collectively the impact of XLID is significant because patients usually are unable to fully participate in society.

OBJECTIVE:

To reveal the molecular mechanisms of various intellectual disabilities and to suggest …

Enhancing Human Spermine Synthase Activity By Engineered Mutations, Zhe Zhang, Yueli Zheng, Margo Petukh, Anthony Pegg, Yoshihiko Ikeguchi, Emil Alexov

Publications

Spermine synthase (SMS) is an enzyme which function is to convert spermidine into spermine. It was shown that gene defects resulting in amino acid changes of the wild type SMS cause Snyder-Robinson syndrome, which is a mild-to-moderate mental disability associated with osteoporosis, facial asymmetry, thin habitus, hypotonia, and a nonspecific movement disorder. These disease-causing missense mutations were demonstrated, both in silico and in vitro, to affect the wild type function of SMS by either destabilizing the SMS dimer/monomer or directly affecting the hydrogen bond network of the active site of SMS. In contrast to these studies, here we report an …

Supersoft X-Rays Reveal A Classical Nova In The M31 Globular Cluster Bol 126, M. Henze, W. Pietsch, F. Haberl, M. Della Valle, A. Riffeser, G. Sala, D. Hatzidimitriou, F. Hofmann, Dieter H. Hartmann, J. Koppenhoefer

Publications

Context. Classical novae (CNe) represent the main class of supersoft X-ray sources (SSSs) in the central region of our neighbouring galaxy M 31. Only three confirmed novae and three SSSs have been discovered in globular clusters (GCs) of any galaxy so far, of which one nova and two SSSs (including the nova) were found in M 31 GCs. Aims. To study the SSS state of CNe we carried out a high-cadence X-ray monitoring of the M 31 central area with XMM-Newton and Chandra. This project is supplemented by regular optical monitoring programmes at various observatories. Methods. We analysed X-ray and …

Bright Radio Emission From An Ultraluminous Stellar-Mass Microquasar In M31, Matthew J. Middleton, James C. A. Miller-Jones, Sera Markoff, Rob Fender, Martin Henze, Natasha Hurley-Walker, Anna M. M. Scaife, Timorthy P. Roberts, Dominic Walton, John Carpenter, Jean-Pierre Macquart, Geoffrey C. Bower, Mark Gurwell, Wolfgang Pietsch, Frank Haberl, Jonathan Harris, Michael Daniel, Junayd Miah, Chris Done, John Morgan, Hugh Dickinson, Phil Charles, Vadim Burwitz, Massimo Della Valle, Michael Freyberg, Jochen Greiner, Margarita Hernanz, Dieter H. Hartmann, Despina Hatzidimitriou, Arno Riffeser, Gloria Sala, Stella Seitz, Pablo Reig, Arne Rau, Marina Orio, David Titterington, Keith Grainge

Publications

A subset of ultraluminous X-ray sources (those with luminosities < 10^40 erg s^-1)^1 are thought to be powered by the accretion of gas onto black holes with masses of ~5-20 M⊙, probably via an accretion disc. The X-ray and radio emission are coupled in such Galactic sources, with the radio emission originating in a relativistic jet thought to be launched from the innermost regions near the black hole4,5, with the most powerful emission occurring when the rate of infalling matter approaches a theoretical maximum (the Eddington limit). Only four such maximal sources are known in the Milky Way, and the absorption of soft X-rays in the interstellar medium precludes determining the causal sequence of events that leads to the ejection of the jet. Here we report radio and X-ray observations of a bright new X-ray source whose peak luminosity can exceed 1039 erg s^-1 in the nearby galaxy, M31. The radio luminosity is extremely high and shows variability on a timescale of tens of minutes, arguing that the source is highly compact and powered by accretion close to the Eddington limit onto a stellar mass black hole. Continued radio and X-ray monitoring of such sources should reveal the causal relationship between the accretion flow and the powerful jet emission.

Delphi Web Server: A Comprehensive Online Suite For Electrostatic Calculations Of Biological Macromolecules And Their Complexes., Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia

Publications

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output …

Between Algorithm And Model: Different Molecular Surface Definitions For The Poisson-Boltzmann Based Electrostatic Characterization Of Biomolecules In Solution, Sergio Decherchi, José Colmenares, Chiara Eva Catalano, Michela Spagnuolo, Emil Alexov, Walter Rocchia

Publications

The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric …

In Silico Investigation Of Ph-Dependence Of Prolactin And Human Growth Hormone Binding To Human Prolactin Receptor, Lin Wang, Shawn Witham, Zhe Zhang, Michael E. Hodsdon, Emil Alexov

Publications

Experimental data shows that the binding of human prolactin (hPRL) to human prolactin receptor (hPRLr-ECD) is strongly pH-dependent, while the binding of the same receptor to human growth hormone (hGH) is pH-independent. Here we carry in silico analysis of the molecular effects causing such a difference and reveal the role of individual amino acids. It is shown that the computational modeling correctly predicts experimentally determined pKa’s of histidine residues in an unbound state in the majority of the cases and the pH-dependence of the binding free energy. Structural analysis carried in conjunction with calculated pH-dependence of the binding revealed that …

Using Delphi Capabilities To Mimic Protein's Conformational Reorganization With Amino Acid Specific Dielectric Constants, Lin Wang, Zhe Zhang, Walter Rocchia, Emil Alexov

Publications

Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins. Modeling such changes is a challenge and requires significant amount of computing time. From point of view of electrostatics, these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field, if the cause is insertion or deletion of a charged amino acid. Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. This allows the changes of the folding energy to …